Variation and genetic structure of the endangered Lepus flavigularis (Lagomorpha: Leporidae)

Lepus flavigularis, is an endemic and endangered species, with only four populations inhabiting Oaxaca, México: Montecillo Santa Cruz, Aguachil, San Francisco del Mar Viejo and Santa María del Mar. Nevertheless, human activities like poaching and land use changes, and the low genetic diversity detected with mitochondrial DNA and allozymes in previous studies, have supported the urgent need of management strategies for this species, and suggest the definition of management units. For this, it is necessary to study the genetic structure with nuclear genes, due to their inheritance and high polymorphism, therefore, the objective of this study was to examine the variation and genetic structure of L. flavigularis using nuclear microsatellites. We sampled four populations of L. flavigularis and a total of 67 jackrabbits were captured by night sampling during the period of 2001 to 2006. We obtained the genomic DNA by the phenol-chloroform-isoamyl alcohol method. To obtain the diversity and genetic structure, seven microsatellites were amplified using the Polymerase Chain Reaction (PCR); the amplifications were visualized through electrophoresis with 10 % polyacrylamide gels, dyed with ethidium bromide. Genetic diversity was determined using the software GenAlEx v. 6.4, and genetic structure was obtained with ARLEQUIN v. 3.1; null alleles were evaluated using the program Micro-Checker v.2.2.2. Additionally, a Bayesian analysis was performed with software STRUCTURE v. 2.2.3., and the isolation by distance (IBD) was studied using the program PASSAGE v.2.0.11.6. Our results showed that the genetic variation found was low (HO = 0.30, HE = 0.24) when compared to other jackrabbit species. Fixed alleles and moderate levels of genetic differentiation (FST = 0.18, P = 0.001) were detected among populations, indicating the effect of the genetic drift and limited gene flow. Bayesian clustering analysis revealed two groups: (1) jackrabbits from Montecillo Santa Cruz, and (2) individuals living in Aguachil, San Francisco del Mar Viejo and Santa María del Mar. No evidence was found of isolation by distance. It is possible that the geographic barriers present between populations (e.g. lagoons, human settlements), rather than the geographical distance between them, may explain the observed genetic structure. The inbreeding coefficient was negative (FIS = -0.27, P = 0.03), indicating genetic sub-structure in populations. We suggest two management units based on the genetically closer populations, which will help define precise conservation actions in L. flavigularis. This research is the basis for defining translocation of individuals between populations, nevertheless, a more extensive future study, with specific molecular markers for L. flavigularis, is required. In addition, it is necessary to analyze the barriers that limit the gene flow, since it is urgent to reduce the genetic differentiation between populations and increase the genetic diversity of this species.

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Genetic diversity and gene flow patterns in two riverine plant species with contrasting life-history traits and distributions across a large inland floodplain

Australian Journal of Botany ◽

10.1071/bt20074 ◽

2020 ◽

Vol 68 (5) ◽

pp. 384

Author(s):

William Higgisson ◽

Dianne Gleeson ◽

Linda Broadhurst ◽

Fiona Dyer

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Water Resource ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Geographic Distance ◽

Resource Development ◽

Water Resource Development ◽

Floodplain River

Gene flow is a key evolutionary driver of spatial genetic structure, reflecting demographic processes and dispersal mechanisms. Understanding how genetic structure is maintained across a landscape can assist in setting conservation objectives. In Australia, floodplains naturally experience highly variable flooding regimes that structure the vegetation communities. Flooding plays an important role, connecting communities on floodplains and enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is reduced physical and subsequent genetic connections. This study aimed to identify and compare the population structure and dispersal patterns of tangled lignum (Duma florulenta) and river cooba (Acacia stenophylla) across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semiarid Australia. Tangled lignum occurs on floodplains while river cooba occurs along rivers. Leaves were collected from 144 tangled lignum plants across 10 sites and 84 river cooba plants across 6 sites, on the floodplain of the lower and mid Lachlan River, and the Murrumbidgee River, NSW. DNA was extracted and genotyped using DArTseq platforms (double digest RADseq). Genetic diversity was compared with floodplain-river connection frequency, and genetic distance (FST) was compared with river distance, geographic distance and floodplain-river connection frequency between sites. Genetic similarity increased with increasing floodplain-river connection frequency in tangled lignum but not in river cooba. In tangled lignum, sites that experience more frequent flooding had greater genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in tangled lignum, but not in river cooba. The distribution of river cooba along rivers facilitates regular dispersal of seeds via hydrochory regardless of river level, while the dispersal of seeds of tangled lignum between patches is dependent on flooding events. The genetic impact of water resource development may be greater for species which occur on floodplains compared with species along river channels.

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Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽

10.1371/journal.pone.0243999 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243999

Author(s):

Ke-Xin Zhu ◽

Shan Jiang ◽

Lei Han ◽

Ming-Ming Wang ◽

Xing-Ya Wang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Genetic Relationships ◽

Management Strategies ◽

Geographic Distance ◽

Northern China ◽

Economic Losses ◽

Chilo Suppressalis

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

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High nuclear genetic differentiation, but low chloroplast diversity in a rare species, Aluta quadrata (Myrtaceae), with a disjunct distribution in the Pilbara, Western Australia

Australian Journal of Botany ◽

10.1071/bt16128 ◽

2016 ◽

Vol 64 (8) ◽

pp. 687 ◽

Cited By ~ 5

Author(s):

M. Byrne ◽

D. J. Coates ◽

B. M. Macdonald ◽

M. Hankinson ◽

S. M. McArthur ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Microsatellite Loci ◽

Disjunct Distribution ◽

Chloroplast Gene ◽

Seed Sources ◽

Chloroplast Haplotype ◽

Haplotype Variation

Geographically separated populations may show high levels of genetic differentiation, depending on the levels of current and historical isolation. In the ancient landscape of the Pilbara region, there are few plant species with restricted distributions, and one such species, Aluta quadrata Rye & Trudgen, is restricted to three separate locations on the southern edge of the Hamersley Range. We investigated genetic diversity and differentiation among geographically isolated locations of A. quadrata, using 10 microsatellite loci to assess contemporary genetic structure, and sequences of seven chloroplast gene regions to infer historical isolation. Nuclear genetic diversity was moderate, with moderate to high genetic differentiation among the three locations, and low differentiation among populations within locations. In contrast, there was no detected variation in the chloroplast genome. The high genetic differentiation is consistent with limited contemporary connectivity among the geographically separated locations, although lack of chloroplast haplotype variation indicates that limited connectivity has occurred more recently and is not due to historical isolation. The level of differentiation suggests use of local seed sources for augmentation or establishment of populations within gene flow distance of existing populations, whereas an experimental translocation established on more distant sites could use mixed seed sources to maximise genetic diversity.

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The genetic structure of the spectacled bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers

Journal of Mammalogy ◽

10.1093/jmammal/gyaa082 ◽

2020 ◽

Vol 101 (4) ◽

pp. 1072-1090

Author(s):

Manuel Ruiz-García ◽

Jessica Yanina Arias Vásquez ◽

Héctor Restrepo ◽

Carlos Herney Cáceres-Martínez ◽

Joseph Mark Shostell

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Isolation By Distance ◽

Phylogenetic Analyses ◽

Population Expansion ◽

Sudden Expansion ◽

Population Decrease ◽

Geographical Regions ◽

Show Evidence

Abstract The spectacled bear (Ursidae: Tremarctos ornatus) is an emblematic umbrella species and one of the top carnivores in the Andean mountains. It is also listed as vulnerable by IUCN and as endangered by CITES. We analyzed the genetic structure of this species in nine geographical regions representing the three Andean Cordilleras in Colombia. We sequenced six mitochondrial genes in 115 spectacled bears; a subset of these specimens (n = 61) were genotyped at seven nuclear microsatellites. We addressed three objectives: 1) determine the genetic diversity and historical demographic changes of the spectacled bear in Colombia; 2) determine phylogeographic patterns of genetic divergence among spectacled bear populations in Colombia; and 3) estimate the levels of gene flow among different regions of Colombia. Our analyses show evidence of high mitochondrial genetic diversity in spectacled bears, both in Colombia as well as in each of the nine regions, most particularly Norte de Santander, Nariño, and Antioquia-Córdoba. In addition, we detected population expansion in Colombia that occurred around 24,000 years ago, followed by a population decrease during the last 7,000 years, and a sudden expansion in the last 300 years. Phylogenetic analyses showed few well-supported clades, with some haplotypes detected in all the departments and Colombian Andean Cordilleras, and other haplotypes restricted to certain geographical areas (Antioquia, Norte de Santander, Cundinamarca, and Nariño). We detected significant genetic heterogeneity among some departments and among the three Colombian Andean Cordilleras for both mitochondrial and nuclear genes. Nevertheless, the moderate levels of gene flow estimated from FST statistics suggest that geographical barriers have not been definitive obstacles to the dispersion of the spectacled bear throughout Colombia. Despite these gene flow estimates, significant spatial autocorrelation was detected for spectacled bear in Colombia, where two kinds of spatial patterns were discovered: genetic patches of 144 km of diameter, and isolation by distance among bears separated from 578 to 800 km. The two most northern spectacled bear populations of Colombia (Norte de Santander and Antioquia) also were the two most differentiated. Their distinctiveness may qualify them as distinct Management Units (MUs) in the context of conservation policies for the spectacled bear in Colombia.

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Genetic Divergence of Two Sitobion avenae Biotypes on Barley and Wheat in China

Insects ◽

10.3390/insects11020117 ◽

2020 ◽

Vol 11 (2) ◽

pp. 117

Author(s):

Da Wang ◽

Xiaoqin Shi ◽

Deguang Liu ◽

Yujing Yang ◽

Zheming Shang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Host Plant ◽

Genetic Divergence ◽

Isolation By Distance ◽

Critical Role ◽

Geographic Distance ◽

Sitobion Avenae ◽

Insect Populations

Host plant affinity and geographic distance can play critical roles in the genetic divergence of insect herbivores and evolution of insect biotypes, but their relative importance in the divergence of insect populations is still poorly understood. We used microsatellite markers to test the effects of host plant species and geographic distance on divergence of two biotypes of the English grain aphid, Sitobion avenae (Fabricius). We found that clones of S. avenae from western provinces (i.e., Xinjiang, Gansu, Qinghai and Shaanxi) had significantly higher genetic diversity than those from eastern provinces (i.e., Anhui, Henan, Hubei, Zhejiang and Jiangsu), suggesting their differentiation between both areas. Based on genetic diversity and distance estimates, biotype 1 clones of eastern provinces showed high genetic divergence from those of western provinces in many cases. Western clones of S. avenae also showed higher genetic divergence among themselves than eastern clones. The Mantel test identified a significant isolation-by-distance (IBD) effect among different geographic populations of S. avenae, providing additional evidence for a critical role of geography in the genetic structure of both S. avenae biotypes. Genetic differentiation (i.e., FST) between the two biotypes was low in all provinces except Shaanxi. Surprisingly, in our analyses of molecular variance, non-significant genetic differentiation between both biotypes or between barley and wheat clones of S. avenae was identified, showing little contribution of host-plant associated differentiation to the divergence of both biotypes in this aphid. Thus, it is highly likely that the divergence of the two S. avenae biotypes involved more geographic isolation and selection of some form than host plant affinity. Our study can provide insights into understanding of genetic structure of insect populations and the divergence of insect biotypes.

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Scale-dependent effects of habitat fragmentation on the genetic diversity of Actinidia chinensis populations in China

Horticulture Research ◽

10.1038/s41438-020-00401-1 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Wenhao Yu ◽

Baofeng Wu ◽

Xinyu Wang ◽

Zhi Yao ◽

Yonghua Li ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Habitat Fragmentation ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Distance Effect ◽

Island Population ◽

Actinidia Chinensis ◽

Fine Scale ◽

Broad Scale

Abstract Spatial scale partly explains the differentiated effects of habitat fragmentation on plant biodiversity, but the mechanisms remain unclear. To investigate the effects of habitat fragmentation on genetic diversity at different scales, we sampled Actinidia chinensis Planch. at broad and fine scales, China. The broad-scale sampling included five mountain populations and one oceanic island population (Zhoushan Archipelago), and the fine-scale sampling covered 11 lake islands and three neighboring land populations in Thousand-Island Lake (TIL). These populations were genotyped at 30 microsatellite loci, and genetic diversity, gene flow, and genetic differentiation were evaluated. Genetic differentiation was positively related to geographical distance at the broad scale, indicating an isolation-by-distance effect of habitat fragmentation on genetic diversity. The oceanic population differed from the mainland populations and experienced recent bottleneck events, but it showed high gene flow with low genetic differentiation from a mountain population connected by the Yangtze River. At the fine scale, no negative genetic effects of habitat fragmentation were found because seed dispersal with water facilitates gene flow between islands. The population size of A. chinensis was positively correlated with the area of TIL islands, supporting island biogeography theory, but no correlation was found between genetic diversity and island area. Our results highlight the scale-dependent effects of habitat fragmentation on genetic diversity and the importance of connectivity between island-like isolated habitats at both the broad and fine scales.

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Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Journal of Mammalogy ◽

10.1644/11-mamm-a-344.1 ◽

2012 ◽

Vol 93 (6) ◽

pp. 1512-1524 ◽

Cited By ~ 9

Author(s):

Sarah A. Sonsthagen ◽

Chadwick V. Jay ◽

Anthony S. Fischbach ◽

George K. Sage ◽

Sandra L. Talbot

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Spatial Genetic Structure ◽

Genetic Relationships ◽

Breeding Population ◽

Pacific Walrus ◽

Breeding Populations ◽

The Pacific

Abstract Pacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

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Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago

10.1101/2020.03.23.004622 ◽

2020 ◽

Author(s):

Yuto Taki ◽

Christian E. Vincenot ◽

Yu Sato ◽

Miho Inoue-Murayama

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Haplotype Network ◽

Iucn Red List ◽

The Philippines ◽

Conservation Units ◽

Long Distance ◽

Flying Fox

AbstractThe Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

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Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽

10.1163/15685403-00003680 ◽

2017 ◽

Vol 90 (7-10) ◽

pp. 845-864

Author(s):

Raquel C. Buranelli ◽

Fernando L. Mantelatto

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Dna Barcode ◽

Population Expansion ◽

Haplotype Network ◽

Sudden Expansion ◽

Restricted Gene Flow ◽

Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

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Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum

Journal of Plant Research ◽

10.1007/s10265-021-01364-7 ◽

2022 ◽

Author(s):

Julita Minasiewicz ◽

Emilia Krawczyk ◽

Joanna Znaniecka ◽

Lucie Vincenot ◽

Ekaterina Zheleznaya ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Plastid Dna ◽

Nuclear Microsatellites ◽

Nuclear Ribosomal Dna ◽

Genetic Characteristics ◽

Mycorrhizal Specificity ◽

Mycoheterotrophic Plants

AbstractSome plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (FST = 0.106 for nuclear microsatellites and FST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (Rr = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.

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